Man pages for tmirus/TTT
What the Package Does (One Line, Title Case)
| analyze_clustering | This function analyzes ST data based on clustering generated... |
| build_lassos | Calculate 2D fused-lasso solutionpath for a countmatrix and... |
| calc_BICs | Returns useful information about a fusedlasso model fit This... |
| clean_ids | This function selects spots based on connectivity. Based on... |
| cluster_counts | cluster counts matrix based using louvain clustering based on... |
| coef_error | Helper function for error handling This function was adapted... |
| enrichment_test | perform enrichment testing using topGO and fisher's exact... |
| fill_ids | fill the barcode data frame with artificial entries for... |
| filter_genes | this function returns a table of interesting genes based on... |
| filter_spot_enrichments | this function filters the enrichment matrix for interesting... |
| fused_lasso_complete_fixed_gamma | Building sparse fused lasso models for given genes from their... |
| normalize_counts | this function is a wrapper for sctransform::vst |
| plot_adjustment | This function helps choosing offset and spacing parameters... |
| plot_spot_enrichments | this function plot spatial patterns of enriched GO terms to... |
| prepare_lasso_data | process the lasso counts and ids for conformity with pipeline... |
| process_input | process input data from ST pipeline to make sure they conform... |
| read_image | this function is a wrapper for EBImage function readImage... |
| remove_background | remove background spots (not covered by tissue) from ST data... |
| slide_orientation | this function changes the orientation of the data by... |
| spatial_gene_plots | create spatial plots for the top n.genes genes in a given... |
| spatial_plot | create 2d spatial plots of ST data with optional image data |
| test_spot_enrichment | perform enrichment testing based on differential gene... |
| visualize_genes | This function visualizes the results of the clustering and... |
